Saito said he was shocked by the test results, insisting he had never taken a steroid and there was no need for him to use a masking agent.
Saito added that for the sake of the Japanese team he had chose to leave the athletes' village.
Provisionally suspended, he has agreed to leave the Olympic Village and will not participate in this year's games, the court said.
"I have been trained in anti-doping".
The Japanese Olympic Committee said Saito was tested after training on February 4, just before he went to bed in the athletes village.
Japanese speedskater Kei Saito has tested positive for an unnamed banned substance.
The most notable case of Japanese athletes breaking doping rules came at the 1984 Summer Olympics in Los Angeles when members of the Japanese men's volleyball team tested positive for a stimulant.
"As for the test results this time, the only possibility I can think of is that I accidentally and unconsciously put a banned substance in my mouth", he added.More news: Kim Jong Un invites South's Moon to Pyongyang: Seoul
Saito's only event of the Olympics was slated to be Wednesday's 5,000m short track relay.
"The findings are beyond me and I plan to fight to prove my innocence. And I am very careful of what I eat and what I drink in everyday life", the athlete said.
This is the first doping violation case registered by the CAS Anti-doping Division in PyeongChang. A doping test showed that Saito tested positive for acetazolamide, a diuretic that can hide the use of performance-enhancing drugs.
Tsutomu Kawasaki, Japan's short track coach, said the suspended Olympian "showed a lot of promise at a young age and has been educated on doping".
Saito, who was summoned before a CAS tribunal on Monday, insisted he was innocent of any wrongdoing He was tested before the Games on Jan 29 and found to be drug-free.
Saito will also be barred from any global Skating Union competitions pending further investigation.
According to several reports, 21-year-old Japanese speed skater Kei Saito failed a doping test.